plot_density: Density Plot of beta-Values

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Density Plot of β-Values

Usage

plot_density(
  scm = NULL,
  assay = "score",
  regions = NULL,
  n_cpgs = 25000,
  pheno = NULL,
  col_palette = "RdYlGn",
  show_legend = TRUE,
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
regions	Granges; genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
n_cpgs	integer; Use these many random CpGs for plotting. Default 25000. Set it to NULL to use all - which can be memory expensive. The seed will be set to n_cpgs for consistency.
pheno	string; Col name of colData(m). Will be used as a factor to color different groups
col_palette	string; Name of the RColorBrewer palette to use for plotting.
show_legend	boolean; Display the legend on the plot
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Value

ggplot2 object

Examples

data('scMethrix_data')
plot_density(scm = scMethrix_data)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.